CLB19 - Plant Editosome Database

Summary

Editing Factor:	CLB19
Synonym:	CHLOROPLAST BIOGENESIS 19; Pigment Defective 247; PDE247
Description:	Loss-of-function clb19 mutants present a yellow phenotype with impaired chloroplast development and early seedling lethality under greenhouse conditions; Transcript patterns are profoundly affected in the mutant plants, with a pattern entirely consistent with a defect in activity of the plastid-encoded RNA polymerase; CLB19 belongs to the PLS subfamily of PPR proteins and is essential for the editing and functionality of the subunit A of plastid-encoded RNA polymerase (RpoA) and the catalytic subunit of the Clp protease (ClpP1); In vitro that CLB19 has a specific interaction with these two targets, in spite of their modest sequence similarity; Similar to other editing proteins, the C-terminal E domain of CLB19 is essential for editing but not for RNA binding. Using biomolecular fluorescence complementation, we demonstrated that the E domain of CLB19 interacts with the RNA-interacting protein MORF2/RIP2 but not with MORF9/RIP9; An interesting finding from this analysis was that overexpression of a truncated CLB19 protein lacking the E domain interferes with cell fate during megasporogenesis and the subsequent establishment of a female gametophyte, supporting an important role of plastids in female gametogenesis
Protein Family:	Pentatricopeptide repeat (PPR) protein
Subclass:	E+
Physical Interaction:	MORF2
Construct Structure:	PLS-E-E+
Gene ID & Species:	AT1G05750 (Arabidopsis thaliana)
Edited Gene(s):	rpoA clpP
Editing Type(s):	C-to-U (34)
Publication(s):	[1] Multiple PPR Protein Interactions Are Involved in the RNA Editing System in Arabidopsis Mitochondria and Plastids, Proc Natl Acad Sci U S A, 2017. [doi:10.1073/pnas.1705815114] [2] Functional analysis of the Arabidopsis thaliana CHLOROPLAST BIOGENESIS 19 pentatricopeptide repeat editing protein, New Phytologist, 2015. [doi:10.1111/nph.13468] [3] Predictable alteration of sequence recognition by RNA editing factors from Arabidopsis, Plant Cell, 2015. [doi:10.1105/tpc.114.134189] [4] CLB19, a pentatricopeptide repeat protein required for editing of rpoA and clpP chloroplast transcripts, The Plant Journal, 2008. [doi:10.1111/j.1365-313X.2008.03634.x]

Editing Details

Species

Gene ID

Organelle

Edited Gene

Position

Region

Nuclear Genome

Organelle Genome

Other Region

Other Position

Editing Type

Codon

Amino Acid

Molecular Effect

Experiment Details

Arabidopsis thaliana

AT1G05750

Chloroplast

clpP

559

CDS

C-to-U

CAU=>UAU
CAC=>UAC
NA=>NA

H=>Y
NA=>NA

Recoding
NA

**Experiment Details**
Genotype (Ecotype)	Allele	Treatment	Treatment Detail	Mutant Type	Phenotype	Tissue	Development Stage	Detection Method	Editing Frequency	Editing Extent	Mutant Effect	PMID
NA	clb19-1	T-DNA Insertion	T-DNA is inserted at codon 230	NA	Pale-yellow cotyledons and seedling leaves when grown under standard light conditions and dies shortly afterwards	Seedling	NA	Poisoned Primer Extension (PPE) Assay	0.00%	Unedited	Absent	18657233
SALK_123752	clb19-3	T-DNA Insertion	NA	NA	Seedlings with a pale-yellow phenotype	Seedling	NA	Poisoned Primer Extension (PPE) Assay	0.00%	Unedited	Absent	18657233
Col-0	Col-0	Control	Control	No mutant	Normal	Seedling	NA	Poisoned Primer Extension (PPE) Assay	NA	High	None	18657233
NA	TC	Complementation	NA	NA	NA	Seedling	NA	Poisoned Primer Extension (PPE) Assay	NA	High	Restored	18657233
NA	CLB19-His	Overexpression	NA	NA	NA	NA	NA	Gel electrophoretic mobility shift assays	NA	NA	NA	25980341
NA	CLB19△E-His	Overexpression	NA	NA	NA	NA	NA	Gel electrophoretic mobility shift assays	NA	NA	NA	25980341
Col-0	WT	Control	Control	No mutant	Normal	Leaf	NA	RT-PCR and calculated with the DNADynamo software (BlueTract	67.00%	High	None	28761003
Col-0	DYW2-GFP-OE1	Generating Arabidopsis plants overexpressing the GFP-tagged DYW2 gene	Col-0 A. thaliana plants were transformed with the 35S::DYW2-GFP plasmids (in pK7WGF2 backbone) by the floral-dip method. Transformed plants were selected based on Kanamycin resistance. Two independen	NA	Slow growth	Leaf	NA	RT-PCR and calculated with the DNADynamo software (BlueTract	7.00%	Poor	Decreased	28761003
Col-0	DYW2-GFP-OE2	Generating Arabidopsis plants overexpressing the GFP-tagged DYW2 gene	Col-0 A. thaliana plants were transformed with the 35S::DYW2-GFP plasmids (in pK7WGF2 backbone) by the floral-dip method. Transformed plants were selected based on Kanamycin resistance. Two independen	NA	Slow growth	Leaf	NA	RT-PCR and calculated with the DNADynamo software (BlueTract	1.00%	Poor	Decreased	28761003

Arabidopsis thaliana

AT1G05750

Plastid

clpP

C-to-U

NA=>NA

**Experiment Details**
Genotype (Ecotype)	Allele	Treatment	Treatment Detail	Mutant Type	Phenotype	Tissue	Development Stage	Detection Method	Editing Frequency	Editing Extent	Mutant Effect	PMID
Col-0	WT	Control	Control	No mutant	NA	NA	3 weeks	Poisoned primer extension (PPE) analysis	89.33%	High	None	25649437
SALK_104250	CLB19wt	Complemented	Plants transformed with wild-type CLB19 driven by the same promoter as used to drive expression of the variants.	NA	NA	NA	3 weeks	Poisoned primer extension (PPE) analysis	89.80%	High	Restored	25649437
SALK_104250	S2[TD]	A T-DNA insertion	A T-DNA insertion (SALK_104250) in At1g05750	NA	NA	NA	3 weeks	Poisoned primer extension (PPE) analysis	89.00%	High	Similar	25649437
SALK_104250	S2[TN]	A T-DNA insertion	A T-DNA insertion (SALK_104250) in At1g05750	NA	NA	NA	3 weeks	Poisoned primer extension (PPE) analysis	87.17%	High	Similar	25649437
SALK_104250	S2[SD]	A T-DNA insertion	A T-DNA insertion (SALK_104250) in At1g05750	NA	NA	NA	3 weeks	Poisoned primer extension (PPE) analysis	51.67%	Medium	Decreased	25649437
SALK_104250	S3[TT]	A T-DNA insertion	A T-DNA insertion (SALK_104250) in At1g05750	NA	NA	NA	3 weeks	Poisoned primer extension (PPE) analysis	40.17%	Medium	Decreased	25649437
SALK_104250	S3[TD]	A T-DNA insertion	A T-DNA insertion (SALK_104250) in At1g05750	NA	NA	NA	3 weeks	Poisoned primer extension (PPE) analysis	20.67%	Low	Decreased	25649437
SALK_104250	c19	A T-DNA insertion	A T-DNA insertion (SALK_104250) in At1g05750	NA	NA	NA	3 weeks	Poisoned primer extension (PPE) analysis	0.00%	Unedited	Absent	25649437

Arabidopsis thaliana

AT1G05750

Chloroplast

rpoA

200

CDS

C-to-U

UCU=>UUU
NA=>NA

S=>F
NA=>NA

Recoding
NA

**Experiment Details**
Genotype (Ecotype)	Allele	Treatment	Treatment Detail	Mutant Type	Phenotype	Tissue	Development Stage	Detection Method	Editing Frequency	Editing Extent	Mutant Effect	PMID
NA	clb19-1	T-DNA Insertion	T-DNA is inserted at codon 230	NA	Pale-yellow cotyledons and seedling leaves when grown under standard light conditions and dies shortly afterwards	Seedling	NA	Poisoned Primer Extension (PPE) Assay	0.00%	Unedited	Absent	18657233
SALK_123752	clb19-3	T-DNA Insertion	NA	NA	Seedlings with a pale-yellow phenotype	Seedling	NA	Poisoned Primer Extension (PPE) Assay	0.00%	Unedited	Absent	18657233
Col-0	Col-0	Control	Control	No mutant	Normal	Seedling	NA	Poisoned Primer Extension (PPE) Assay	NA	High	None	18657233
NA	TC	Complementation	NA	NA	NA	Seedling	NA	Poisoned Primer Extension (PPE) Assay	NA	High	Restored	18657233
NA	CLB19-His	Overexpression	NA	NA	NA	NA	NA	Gel electrophoretic mobility shift assays	NA	NA	NA	25980341
NA	CLB19△E-His	Overexpression	NA	NA	NA	NA	NA	Gel electrophoretic mobility shift assays	NA	NA	NA	25980341
Col-0	WT	Control	Control	No mutant	Normal	Leaf	NA	RT-PCR and calculated with the DNADynamo software (BlueTract	74.00%	High	None	28761003
Col-0	DYW2-GFP-OE1	Generating Arabidopsis plants overexpressing the GFP-tagged DYW2 gene	Col-0 A. thaliana plants were transformed with the 35S::DYW2-GFP plasmids (in pK7WGF2 backbone) by the floral-dip method. Transformed plants were selected based on Kanamycin resistance. Two independen	NA	Slow growth	Leaf	NA	RT-PCR and calculated with the DNADynamo software (BlueTract	4.00%	Poor	Decreased	28761003
Col-0	DYW2-GFP-OE2	Generating Arabidopsis plants overexpressing the GFP-tagged DYW2 gene	Col-0 A. thaliana plants were transformed with the 35S::DYW2-GFP plasmids (in pK7WGF2 backbone) by the floral-dip method. Transformed plants were selected based on Kanamycin resistance. Two independen	NA	Slow growth	Leaf	NA	RT-PCR and calculated with the DNADynamo software (BlueTract	5.00%	Poor	Decreased	28761003

Arabidopsis thaliana

AT1G05750

Plastid

rpoA

C-to-U

NA=>NA

**Experiment Details**
Genotype (Ecotype)	Allele	Treatment	Treatment Detail	Mutant Type	Phenotype	Tissue	Development Stage	Detection Method	Editing Frequency	Editing Extent	Mutant Effect	PMID
Col-0	WT	Control	Control	No mutant	NA	NA	3 weeks	Poisoned primer extension (PPE) analysis	75.67%	High	None	25649437
SALK_104250	CLB19wt	Complemented	Plants transformed with wild-type CLB19 driven by the same promoter as used to drive expression of the variants.	NA	NA	NA	3 weeks	Poisoned primer extension (PPE) analysis	78.80%	High	Restored	25649437
SALK_104250	S2[TD]	A T-DNA insertion	A T-DNA insertion (SALK_104250) in At1g05750	NA	NA	NA	3 weeks	Poisoned primer extension (PPE) analysis	69.17%	High	Similar	25649437
SALK_104250	S2[TN]	A T-DNA insertion	A T-DNA insertion (SALK_104250) in At1g05750	NA	NA	NA	3 weeks	Poisoned primer extension (PPE) analysis	72.67%	High	Similar	25649437
SALK_104250	S2[SD]	A T-DNA insertion	A T-DNA insertion (SALK_104250) in At1g05750	NA	NA	NA	3 weeks	Poisoned primer extension (PPE) analysis	49.80%	Medium	Decreased	25649437
SALK_104250	S3[TT]	A T-DNA insertion	A T-DNA insertion (SALK_104250) in At1g05750	NA	NA	NA	3 weeks	Poisoned primer extension (PPE) analysis	73.17%	High	Similar	25649437
SALK_104250	S3[TD]	A T-DNA insertion	A T-DNA insertion (SALK_104250) in At1g05750	NA	NA	NA	3 weeks	Poisoned primer extension (PPE) analysis	78.00%	High	Similar	25649437
SALK_104250	c19	A T-DNA insertion	A T-DNA insertion (SALK_104250) in At1g05750	NA	NA	NA	3 weeks	Poisoned primer extension (PPE) analysis	0.33%	Poor	Decreased	25649437